[BioC] .Rnw file

[Lana Schaffer]

Wolfgang,
> Can you please try with tilingArray from the development branch
> http://www.bioconductor.org/packages/2.0/bioc/html/tilingArray.html
> and see if you can reproduce this?

Warning message:
package 'tilingArray' was built under R version 2.5.0

Error:  chunk 8 (label=normalizeByReference)
Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose = verbose) 
:

The likelihood optimization did not converge. A likely reason is that the 
normalization parameters are not uniquely identifiable from the provided 
data.
Possibly, the columns of the data matrix are exactly co-linear or affine 
dependent - please verify the data to make sure there were no mix-ups.

Enter a frame number, or 0 to exit

1: Sweave("assessNorm.Rnw")
2: driver$runcode(drobj, chunk, chunkopts)
3: RweaveTryStop(err, options)

Lana
----- Original Message ----- 
From: "Wolfgang Huber" <huber at ebi.ac.uk>
To: "Lana Schaffer" <schaffer at scripps.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Wednesday, January 03, 2007 4:11 PM
Subject: Re: [BioC] .Rnw file


> Dear Lana,
>
> Can you please try with tilingArray from the development branch
> http://www.bioconductor.org/packages/2.0/bioc/html/tilingArray.html
> and see if you can reproduce this?
>
> I have no idea what could cause your problem reported below, and have not 
> seen it before (however I have never used the Windows-version of R for 
> this).
>
> Has anyone else seen this error for these data?
>
>   Best wishes
>     Wolfgang
>
>
>
>> Wolfgand,
>>> sessionInfo()
>> R version 2.4.0 (2006-10-03)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
>> States.1252;LC_MONETARY=English_United 
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] "splines"   "grid"      "tools"     "methods"   "stats" 
>> "graphics" "grDevices" "utils"
>> [9] "datasets"  "base"
>>
>> other attached packages:
>> davidTiling           GO  tilingArray       pixmap  geneplotter annotate 
>> genefilter     survival
>>     "1.0.4"     "1.14.1"     "1.12.0"      "0.4-5"     "1.12.0" "1.12.1" 
>> "1.12.0"       "2.29"
>>         vsn  strucchange     sandwich          zoo RColorBrewer affy 
>> affyio      Biobase
>>    "1.12.0"      "1.3-1"      "2.0-1"      "1.2-1"      "0.2-3" "1.12.2" 
>> "1.2.0"     "1.12.2"
>>>
>> Thanks,
>> Lana
>> ----- Original Message ----- From: "Wolfgang Huber" <huber at ebi.ac.uk>
>> To: "Lana Schaffer" <schaffer at scripps.edu>
>> Cc: <bioconductor at stat.math.ethz.ch>
>> Sent: Wednesday, January 03, 2007 12:50 PM
>> Subject: Re: [BioC] .Rnw file
>>
>>
>>>
>>> Dear Lana,
>>> what is the output of "sessionInfo()"?
>>>  Best wishes
>>>   Wolfgang
>>>
>>>
>>> Lana Schaffer wrote:
>>>> Steffen,
>>>>> Sweave("assessNorm.Rnw")
>>>>> Sweave("assessNorm.Rnw")
>>>> Writing to file assessNorm.tex
>>>> Processing code chunks ...
>>>>  1 : echo term hide (label=load)
>>>>  2 : term verbatim (label=errorReporting)
>>>>  3 : echo term verbatim (label=showDavidTilingData)
>>>>  4 : echo term verbatim (label=probeAnno)
>>>>  5 : echo term verbatim (label=whPM)
>>>>  6 : echo term verbatim (label=table)
>>>>  7 : echo term verbatim (label=selectArrays)
>>>>  8 : echo term verbatim (label=normalizeByReference)
>>>>
>>>> Error:  chunk 8 (label=normalizeByReference)
>>>> Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose = 
>>>> verbose) :
>>>>
>>>> The likelihood optimization did not converge. A likely reason is that 
>>>> the normalization parameters are not uniquely identifiable from the 
>>>> provided data.
>>>> Possibly, the columns of the data matrix are exactly co-linear or 
>>>> affine dependent - please verify the data to make sure there were no 
>>>> mix-ups.
>>>>
>>>> Enter a frame number, or 0 to exit
>>>>
>>>> 1: Sweave("assessNorm.Rnw")
>>>> 2: driver$runcode(drobj, chunk, chunkopts)
>>>> 3: RweaveTryStop(err, options)
>>>>
>>>> ----- Original Message ----- From: "Steffen Durinck" 
>>>> <durincks at mail.nih.gov>
>>>> To: "Lana Schaffer" <schaffer at scripps.edu>
>>>> Cc: <bioconductor at stat.math.ethz.ch>
>>>> Sent: Wednesday, January 03, 2007 10:55 AM
>>>> Subject: Re: [BioC] .Rnw file
>>>>
>>>>
>>>>> Hi Lana,
>>>>>
>>>>> Try:
>>>>>
>>>>> Sweave("assessNorm.Rnw")
>>>>>
>>>>> best,
>>>>> Steffen
>>>>>
>>>>> Lana Schaffer wrote:
>>>>>> Hi,
>>>>>> I am a little confused how to use the .Rnw file to make a vignette.
>>>>>> Instructions say "source file inst/scripts/assessNorm.Rnw"
>>>>>> but when I use the command :  source("assessNorm.Rnw")
>>>>>> I get an error:
>>>>>> Error in parse(file, n = -1, NULL, "?") : syntax error at
>>>>>> 1: %\VignetteIndexEntry{tilingArray - assess normalization}
>>>>>>
>>>>>> probably because it is not an R file.
>>>>>> Would you straighten me out a bit?
>>>>>>
>>>>>> Lana Schaffer
>>>>>> Biostatistics/Informatics
>>>>>> The Scripps Research Institute
>>>>>> DNA Array Core Facility
>>>>>> La Jolla, CA 92037
>>>>>> (858) 784-2263
>>>>>> (858) 784-2994
>>>>>> schaffer at scripps.edu
>>>>>>
>>>>>>
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
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>>>>>>
>>>>>
>>>>
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>>>
>>>
>>> -- 
>>> ------------------------------------------------------------------
>>> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>>>
>
>
> -- 
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>